Microbial Cell Factories最新文献

{"title":"Multiplex metabolic engineering of yeast for high-efficiency all-trans-retinoic acid production.","authors":"Wenhao Li, Dong Wang, Tingting Yang, Xiaochen Ma, Xueli Zhang, Zhubo Dai","doi":"10.1186/s12934-025-02782-1","DOIUrl":"10.1186/s12934-025-02782-1","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"157"},"PeriodicalIF":4.3,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of the tagatose catabolic gene cluster and development of a tagatose-inducible expression system in the probiotic Escherichia coli Nissle 1917.","authors":"Keunha Park, Youngshin Kim, Dohyeon Kim, Su Min Oh, Tae Jeong Koo, Seung Min Yoo, Sung Ho Yoon","doi":"10.1186/s12934-025-02771-4","DOIUrl":"10.1186/s12934-025-02771-4","url":null,"abstract":"<p><strong>Background: </strong>The probiotic Escherichia coli Nissle 1917 (EcN) is a promising microbial chassis for therapeutic and industrial applications. However, its broad utility is limited by a lack of reliable inducible gene expression systems that precisely control gene expression.</p><p><strong>Results: </strong>We developed a tagatose-inducible expression system in EcN using D-tagatose, a naturally occurring sugar with established safety in humans, as a metabolizable inducer. Through differential RNA sequencing and sequence analysis, we identified the key regulatory elements governing D-tagatose catabolism in EcN and demonstrated that the DeoR family regulator (TagR) functions as a tagatose-responsive repressor. The developed system exhibited a strong dose-dependent response to D-tagatose, ensuring uniform and tunable gene activation across cell populations. Additionally, a catabolite repression-enabled auto-induction strategy facilitated robust biomass accumulation, followed by targeted protein production. This expression system was successfully applied to overexpress recombinant proteins under both aerobic and anaerobic conditions.</p><p><strong>Conclusions: </strong>D-Tagatose is a naturally occurring low-calorie sugar that can serve as an inducer in vivo, including within the human gut microbiome. Thus, the tagatose-inducible expression system provides EcN with an additional tunable option for gene regulation, which may be valuable in applications such as synthetic biology and metabolic engineering.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"158"},"PeriodicalIF":4.3,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Streamlined production of immobilized D-psicose 3-epimerase via secretion in Pichia pastoris: a new paradigm for industrial D-psicose production.","authors":"Pimsiriya Srila, Phitsanu Pinmanee, Boontiwa Ninchan, Nisit Watthanasakphuban","doi":"10.1186/s12934-025-02763-4","DOIUrl":"10.1186/s12934-025-02763-4","url":null,"abstract":"<p><strong>Background: </strong>D-psicose, a rare sugar with significant health benefits, holds great promise as a low-calorie sweetener. Its synthesis requires the enzyme called D-psicose 3-epimerase (DPEase), which converts D-fructose into D-psicose. This study focuses on an alternative protein expression system for secretion DPEase production, using Pichia pastoris KM71. The gene encoding DPEase from Bacillus sp. KCTC 13219 was codon-optimized and fused downstream of the α-factor signal peptide. A one-step purification and immobilization method was developed by directly binding crude DPEase to a His-tag affinity column, enhancing both enzyme stability and reusability.</p><p><strong>Results: </strong>The recombinant DPEase was successfully expressed in P. pastoris and efficiently secreted into the culture medium, simplifying downstream processing. The purified DPEase exhibited optimal activity at pH 6.0 and 60 °C, demonstrating remarkable thermostability and maintaining over 80% relative activity across a broad pH range (pH 5.0-11.0) and temperature range (35-70 °C). Purification with 200 mM imidazole elution resulted in a 12.54-fold increase in the purification factor, achieving a specific activity of 3.65 Units/mg. The maximum D-psicose conversion rate of purified DPEase was 17.03% at 120 min reaction with 10% (w/v) D-fructose. The developed DPEase immobilization system showed high binding efficiency, facilitating one-step purification and immobilization for ready-to-use DPEase column. The immobilized enzyme could be reused up to five cycles, maintaining 83.38% relative activity, highlighting the potential of this system for efficient D-psicose production.</p><p><strong>Conclusions: </strong>This study successfully developed a prototype system for extracellular DPEase production in a recombinant microorganism. This streamlined enzyme purification and immobilization, significantly reducing the DPEase production costs. The recombinant DPEase exhibited remarkable stability across a wide range of pH and temperature. This broad stability makes the enzyme highly promising for industrial-scale D-psicose production, resulting in reduced energy costs and simplified synthesis process. The DPEase demonstrated desirable properties for various D-psicose conversion conditions, and the immobilized enzyme exhibited efficient reusability. These findings support the potential application of this system for large-scale production of D-psicose, a rare sugar with promising uses in the food and pharmaceutical industries.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"149"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cis,cis-muconic acid production from lignin related molecules byAcinetobacter baylyi ADP1.","authors":"Changshuo Liu, Vilja Juvonen, Ella Meriläinen, Elena Efimova, Jin Luo, Milla Salmela, Suvi Santala, Ville Santala","doi":"10.1186/s12934-025-02780-3","DOIUrl":"10.1186/s12934-025-02780-3","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"150"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De novo biosynthesis of taxifolin in yeast peroxisomes.","authors":"Qi Wu, Ruibing Chen, Lei Zhang","doi":"10.1186/s12934-025-02773-2","DOIUrl":"10.1186/s12934-025-02773-2","url":null,"abstract":"<p><strong>Background: </strong>Yeast peroxisomes have been engineered as ideal synthetic compartments to enhance the heterologous biosynthesis of natural products, particularly terpenoids and fatty acid derivatives. This advantage is primarily attributed to the rich acetyl-CoA pool generated from the spatially specific fatty acid β-oxidation within peroxisomes. However, their potential for flavonoid biosynthesis has been largely underexplored, primarily due to limited knowledge regarding precursor transport, cofactor availability, and the redox environment in peroxisomes.</p><p><strong>Results: </strong>In this study, we successfully compartmentalized the biosynthesis of taxifolin, a dihydroflavonol, in Saccharomyces cerevisiae peroxisomes. The result indicated that flavonoid biosynthesis in peroxisome offers a more efficient approach compared to its synthesis in the cytosol. This study managed to expand the application scope of peroxisome compartmentalization to flavonoid biosynthesis. By reinforcing the rate-limiting steps, optimizing cofactor supply and activation of fatty acids, we accomplished the de novo synthesis of taxifolin in peroxisomes for the first time, attaining a titer of 120.3 ± 2.4 mg/L in shake-flask fermentation using a minimal medium.</p><p><strong>Conclusion: </strong>These findings highlight the feasibility of peroxisomal compartmentalization for flavonoid biosynthesis, providing new insights and a framework for the biosynthesis of other high-value flavonoids using yeast peroxisomes.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"153"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel function of ribosomal protein RPL14B: regulation of CdSe quantum dots biosynthesis in living Saccharomyces cerevisiae cells.","authors":"Jiye Liu, Yong Li, Jiawei Tu, Daiwen Pang, Lipeng Zhong, Zhixiong Xie","doi":"10.1186/s12934-025-02777-y","DOIUrl":"10.1186/s12934-025-02777-y","url":null,"abstract":"<p><p>Biosynthesis of CdSe quantum dots is the process of converting metal ions into semiconductor nanomaterials. Studies have shown that CdSe quantum dots synthesized by Saccharomyces cerevisiae are rich in ribosomal proteins, but the role of ribosomal proteins in the synthesis of CdSe quantum dots remains unclear. In this paper, ribosomal proteins enriched during the synthesis of CdSe quantum dots by S. cerevisiae were screened, and their effects on the synthesis of quantum dots were detected by gene knockout and over-expression. The results reveal that ribosomal protein RPL14B is involved in the synthesis of quantum dots. RPL14B binds cadmium ions during the nucleation of CdSe quantum dots and acts as a template, ultimately regulating the particle size of CdSe quantum dots by change the incubation time of CdCl₂. In summary, this study elucidates the mechanism of ribosomal protein RPL14B regulation of CdSe quantum dot biosynthesis, laying a foundation for the precise regulation of CdSe quantum dot synthesis.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"152"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-driven enhanced hydrocarbon emulsification in an environmental Pseudomonas aeruginosa strain.","authors":"Luis M Salazar-García, Luis C Damas-Ramos, Luisa M Trejo-Alarcón, Daniela Rago, Linda Ahonen, Pablo Cruz-Morales, Patricia Ponce-Noyola, Cuauhtémoc Licona-Cassani","doi":"10.1186/s12934-025-02769-y","DOIUrl":"10.1186/s12934-025-02769-y","url":null,"abstract":"<p><strong>Background: </strong>Oil spills are a major concern due to the economic impact and severe effects on the ecosystem. To mitigate oil spills, hydrocarbon dispersion through emulsification is a promising approach, as it makes oil more susceptible to degradation by microorganisms. Environmental strains of Pseudomonas aeruginosa have demonstrated significant potential for producing rhamnolipids (RMLs) and pyocyanin (PYO), secondary metabolites associated to hydrocarbon emulsification. In this study, we isolated and characterized an environmental strain from an oil-contaminated site in the Gulf of Mexico. Upon genome sequencing and taxonomic classification, we developed genetic engineering tools and assessed their capacity to produce PYO and RMLs, molecules relevant for hydrocarbon emulsification.</p><p><strong>Results: </strong>Using the CRISPR/Cas9-APOBEC1-UGI system, we generated a targeted cytosine to thymine transition in the rpoS gene to generate a premature STOP codon. The resulting mutant exhibited increased production of PYO and RMLs, along with enhanced gasoline emulsification in cell-free supernatants, demonstrating successful modulation of a key regulatory gene. While the strain IGLPR01 retains certain virulence-associated features, this study contributes to the exploration of environmental isolates as future candidate chassis for biosurfactant production, emphasizing the need for further safety evaluation and rational attenuation strategies.</p><p><strong>Conclusion: </strong>This study provides a successful example of implementing CRISPR-based editing in an environmental P. aeruginosa strain. Despite the technical challenges, a genetic editing system was established and validated through a proof of concept to increase production of relevant metabolites. Our work demonstrates the applicability of genetic engineering tools in non-model environmental isolates, facilitating further developments. Importantly, the presence of virulence-associated features highlights the need for in-depth evaluation of pathogenicity and containment strategies before considering any future biotechnological applications.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"151"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient biodegradation and detoxification of reactive black 5 using a newly constructed bacterial consortium.","authors":"Manar K Abd Elnabi, Mohamed A Ghazy, Sameh S Ali, Marwa Eltarahony, Amr Nassrallah","doi":"10.1186/s12934-025-02768-z","DOIUrl":"10.1186/s12934-025-02768-z","url":null,"abstract":"<p><p>The release of azo dyes into wastewater from textile industries poses a significant environmental challenge due to their toxicity and recalcitrance. Among these dyes, Reactive Black 5 (RB5) is one of the most widely used and environmentally persistent due to its complex aromatic structure, high stability, and extensive use in the textile sector. This study aimed to develop and optimize a highly efficient bacterial consortium for the decolorization and detoxification of RB5. Three bacterial species-Bacillus cereus, Proteus mirabilis, and Stenotrophomonas maltophilia-were isolated from industrial effluents and combined into a consortium based on compatibility testing. The optimization of cultural and incubation conditions using Plackett-Burman Design (PBD) and Central Composite Design (CCD) significantly enhanced RB5 decolorization efficiency, reaching 98.56% under static conditions. Enzymatic analysis revealed the crucial role of NADH-DCIP reductase and azoreductase in azo bond cleavage, while oxidative enzymes facilitated further degradation into non-toxic metabolites. Metabolite characterization using UV-Vis, FTIR, and GC-MS confirmed the breakdown of RB5 into intermediate compounds with reduced toxicity. Toxicity assessments demonstrated a 66.38-21.38% reduction in root growth inhibition, an increase in germination rate from 40 to 93.33%, a decrease in Artemia salina mortality from 86.7 to 23.3%, and a reduction in cytotoxicity from 55.31 to 14.45% in human breast epithelial cells. These findings demonstrate the potential of the developed consortium as an eco-friendly, cost-effective solution for RB5-contaminated wastewater. Future studies should focus on pilot-scale implementation, long-term stability under variable effluent conditions, and regulatory compliance for industrial deployment.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"154"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protease production by Serratia liquefaciens NRC1 using fish gut waste as a sustainable approach to antimicrobial peptide generation and combating Candida auris acquired resistance.","authors":"Shaymaa A Ismail, Heba M Shalaby, Amira A Hassan, Marwa Mahmoud, Bahgat Fayed","doi":"10.1186/s12934-025-02767-0","DOIUrl":"10.1186/s12934-025-02767-0","url":null,"abstract":"<p><strong>Background: </strong>The global rise of antimicrobial resistance has accelerated the search for sustainable and eco-friendly therapeutic alternatives. This study evaluates fish gut waste (FGW) as a low-cost, renewable substrate for producing antifungal peptides through the proteolytic activity of Serratia liquefaciens NRC1.</p><p><strong>Result: </strong>Optimization of protease production using statistical designs resulted in a fourfold increase in enzyme yield. The protease demonstrated stability at neutral pH and moderate temperatures (40-50 °C), and efficiently hydrolyzed complex proteins such as collagen and keratin. Peptides generated from FGW hydrolysis exhibited significant antifungal activity against Candida auris (C. auris), with a MIC₅₀ of 5.1 ± 0.08 mg/ml. Unlike fluconazole, repeated peptide exposure did not induce resistance, nor did it alter the expression levels of key resistance genes (CDR1, ERG11), as confirmed by qRT-PCR. Peptide profiling using MALDI-TOF/MS, coupled with in silico analysis via AMPfun, identified multiple candidates with predicted antifungal properties.</p><p><strong>Conclusion: </strong>This research highlights the potential of fish gut waste-derived peptides as a sustainable and effective antifungal strategy against C. auris, offering an alternative to conventional antifungal drugs.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"155"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sortase-mediated surface display of a chimeric immunogen on Bacillus subtilis: a chicken necrotic enteritis vaccine candidate.","authors":"Bassima Al-Aneed, Hoang Duc Nguyen, Ali Akbar Masoudi, Saghi Nooraei, Abbas Hajizade, Hossein Tarrahimofrad, Gholamreza Ahmadian, Jamshid Razmyar, Moeen Khatami","doi":"10.1186/s12934-025-02762-5","DOIUrl":"10.1186/s12934-025-02762-5","url":null,"abstract":"<p><p>The application of sortase-mediated surface display technology on Bacillus subtilis represents a novel approach in protein engineering. We developed and evaluated a recombinant chimeric protein (R-anz) integrating truncated forms of three Clostridium perfringens toxins (CPA, NetB, ZMP) displayed on B. subtilis. Bioinformatics analyses using docking demonstrated that the 3D structure of R-anz chimeric protein has the potential to interact with chicken Toll-like receptor 21 (TLR21). Successful expression of the chimeric antigen was confirmed through SDS-PAGE and Western blotting, revealing a 78 kDa band in lysozyme-treated, xylose-induced samples. Oral immunization of chickens with this live bacterial vaccine significantly elevated IgY antibody levels, as assessed by ELISA. Cytokine profiling demonstrated a robust immune response, with marked upregulation of IFN-γ, IL-4, IL-17, and IL-22. Post-challenge with virulent C. perfringens strains, immunized chickens exhibited significantly reduced intestinal lesion scores, indicating partial protection. This study highlights the dual activation of humoral and cellular immune pathways, evidenced by elevated IgY levels and enhanced cytokine responses, particularly IFN-γ, IL-4, and IL-22. While the results demonstrate the potential of the R-anz chimeric protein to mitigate necrotic enteritis (NE), further research is essential to refine its efficacy, explore commercial feasibility, and address industry-specific challenges. This work paves the way for advancing NE vaccines using innovative sortase-mediated surface display technology, offering a promising strategy for sustainable poultry health management.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"147"},"PeriodicalIF":4.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}